What is the difference between thinking of you and thinking about you?

There is not much difference. They can, in fact, mean the same thing, but "thinking of you" is used more when one is thinking about what would please or help the other person. "When I saw your favourite candy in the store, I couldn't help thinking of you." "Thinking about you" does not always have this positive connotation. "I was thinking about you when they asked who had alibis at the time of the murder. You didn't, did you?"